Accepting PhD Students

PhD projects

Bioinformatics, computational biology, machine learning, pattern recognition, biomedical big data

20042020

Research output per year

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Research Output

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Conference Paper
2020

PhosTransfer: a deep transfer learning framework for kinase-specific phosphorylation site prediction in hierarchy

Xu, Y., Wilson, C., Leier, A., Marquez-Lago, T. T., Whisstock, J. & Song, J., 2020, Advances in Knowledge Discovery and Data Mining: 24th Pacific-Asia Conference, PAKDD 2020 Singapore, May 11–14, 2020 Proceedings, Part II. Lauw, H. W., Wong, R. C-W., Ntoulas, A., Lim, E-P., Ng, S-K. & Pan, S. J. (eds.). Cham Switzerland: Springer, p. 384-395 12 p. (Lecture Notes in Computer Science; vol. 12085 ).

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Open Access
File
2017

Collaborative data analytics towards prediction on pathogen-host protein-protein interactions

Chen, H., Shen, J., Wang, L. & Song, J., 12 Oct 2017, 2017 IEEE 21st International Conference on Computer Supported Cooperative Work in Design (CSCWD). Shen, W., Antunes, P., Thuan, N. H., Barthes, J-P., Luo, J. & Yong, J. (eds.). 1st ed. IEEE, Institute of Electrical and Electronics Engineers, p. 269-274 6 p. 8066706

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

3 Citations (Scopus)

Leveraging Stacked Denoising Autoencoder in Prediction of Pathogen-Host Protein-Protein Interactions

Chen, H., Shen, J., Wang, L. & Song, J., 7 Sep 2017, 2017 IEEE International Congress on Big Data: BigData Congress. Karypis, G. & Zhang, J. (eds.). 1st ed. IEEE, Institute of Electrical and Electronics Engineers, p. 368-375 8 p. 8029347

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

6 Citations (Scopus)

Preface

Wang, Y., Burrage, K., Liu, Y., Morishita, S., Tian, T., Jiang, Q., Song, J., Wang, G., Zhu, Q. & Hu, X. T., 17 Jan 2017, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016.

Research output: Chapter in Book/Report/Conference proceedingConference PaperOtherpeer-review

Towards Elucidating the Structural Principles of Host-Pathogen Protein-Protein Interaction Networks: A Bioinformatics Survey

Chen, H., Song, J., Sun, G., Shen, J. & Wang, L., 7 Sep 2017, 2017 IEEE International Congress on Big Data: Big Data Congress. Karypis, G. & Zhang, J. (eds.). 1st ed. IEEE, Institute of Electrical and Electronics Engineers, p. 177-184 8 p. 8029324

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

1 Citation (Scopus)
2016

Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network

Jindalertudomdee, J., Hayashida, M., Song, J. & Akutsu, T., 16 Dec 2016, Proceedings - 2016 IEEE 16th International Conference on Bioinformatics and Bioengineering, BIBE 2016. Piscataway, NJ: IEEE, Institute of Electrical and Electronics Engineers, p. 7-12 6 p. 7789953

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

2 Citations (Scopus)

Towards data analytics of pathogen-host protein-protein interaction: A survey

Chen, H., Shen, J., Wang, L. & Song, J., 5 Oct 2016, Proceedings - 2016 IEEE International Congress on Big Data, BigData Congress 2016. Pu, C., Fox, G. & Damiani, E. (eds.). IEEE, Institute of Electrical and Electronics Engineers, p. 377-388 12 p. 7584966

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

8 Citations (Scopus)
2015

Fabrication of high-Q lithium niobate microresonators using femtosecond laser micromachining for second harmonic generation

Lin, J., Xu, Y., Fang, Z., Wang, M., Song, J., Wang, N., Qiao, L., Fang, W. & Cheng, Y., 10 Aug 2015, 2015 Conference on Lasers and Electro-Optics, CLEO 2015. IEEE, Institute of Electrical and Electronics Engineers, Vol. 2015-August. 7184057

Research output: Chapter in Book/Report/Conference proceedingConference PaperOtherpeer-review

1 Citation (Scopus)
2012

Predicting protein-RNA residue-base contacts using two-dimensional conditional random field

Hayashida, M., Kamada, M., Song, J. & Akutsu, T., 2012, 2012 IEEE 6th International Conference on Systems Biology, ISB 2012. Wu, L-Y. & Horimoto, K. (eds.). USA: IEEE, Institute of Electrical and Electronics Engineers, Vol. 1. p. 152 - 157 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperOtherpeer-review

1 Citation (Scopus)
2011

Discriminative random field approach to prediction of protein residue contacts

Kamada, M., Hayashida, M., Song, J. & Akutsu, T., 2011, 2011 IEEE Conference on Systems Biology (ISB). Chen, L., Zhang, X. S. & Wang, Y. (eds.). China: IEEE, Institute of Electrical and Electronics Engineers, Vol. 2011. p. 285 - 291 7 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

3 Citations (Scopus)

Exploring drug combinations in a drug-cocktail network

Xu, K-J., Hu, F-Y., Song, J. & Zhao, X-M., 2011, 2011 IEEE Conference on Systems Biology (ISB). Chen, L., Zhang, X. S. & Wang, Y. (eds.). China: IEEE, Institute of Electrical and Electronics Engineers, Vol. 2011. p. 382 - 387 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

6 Citations (Scopus)

Predicting functional impact of single amino acid polymorphisms by integrating sequence and structural features

Wang, M., Shen, H-B., Akutsu, T. & Song, J., 2011, 2011 IEEE Conference on Systems Biology 2011. Chen, L., Zhang, X. S. & Wang, Y. (eds.). China: IEEE, Institute of Electrical and Electronics Engineers, p. 18 - 26 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

3 Citations (Scopus)
2010

A Network Biology Approach to Understand Combination of Drugs

Xu, K-J., Song, J. & Zhao, X-M., 2010, The 4th International Conference on Computational Systems Biology (ISB2010). Chen, L., Zhang, X. S. & Wang, Y. (eds.). China: IEEE, Institute of Electrical and Electronics Engineers, p. 347 - 354 8 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Conditional Random Field Approach to Prediction of Protein-Protein Interactions Using Mutual Information Between Domains

Hayashida, M., Kamada, M., Song, J. & Akutsu, T., 2010, The 4th International Conference on Computational Systems Biology (ISB2010). Chen, L., Zhang, X. S. & Wang, Y. (eds.). China: IEEE, Institute of Electrical and Electronics Engineers, p. 276 - 284 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review